bio 221 lect 5pt2 +
what is directional selection
directional selection is when the population evolves toward the fittest genotype, with the allele that offer the highest fitness becoming more common over gens until it reaches fixation
how does the fitness of heterozygotes and homozygotes relate to directional selection
if the fitness of heterozygote is exactly between the fitness of the two homozygotes, the population will move towards the fittest genotype (homozygote) over generatrions
what are the 5 factors affecting the time to fixation in directional selection
1. inital allele frequencies
2. selection coeffcient
3. generation time
4. degree of dominance
5. population size
how do initial allele frequencies affect the time to fixation
rare alleles: take longer to reach fization as they start with low frequency
common alleles: reach fixation due to faster high intial frequency
what is the role of the selection coeffcient in fixation
a larger selection coefficient (s) means a larger fitness advantage, which causes the beenfical allele to rise to fixation more quickly
how does the generation time influence the speed of fixation
species with shorter gen times will see beneficial alleles reach fixation faster than species with longer gen times which take longer to evolve
how does the degree of dominance affect fixation
completely dominant allles rise to fixation fatest since they are expressed in both heterozygotes and homzygotes where as recessive alleles rise slowly at first but then rapidly progress to fixation after reaching a certain frequency
do intermediate (additive) alleles rise fast?
they are slower at first than complete dominant but reach the fixation the fatest becuase both homozygotes express the trait
how does pop size affect the speed of fixation
small pops are more affected by genetic drift which can cause beneficial alleles which are present at a low frequency to be lost by drift/chance because they wont increase in freq
how does the speed of fixation differ with large population s
large pops experience less drift, allowing selection to operate more effciently and benefical alleles to reach fixation faster
how does the relative fitness of alleles change as their freuqnecy increases
as the frequency of either allele A1 or A2 increases, its relative fitness decreases. this means the alllele becomes less fit as it becomes more common in the pop
What is the result of selection when the frequency of an allele increases?
When the frequency of an allele increases, its relative fitness decreases, which leads to a decrease in the allele’s frequency in the population over time. This is a feature of negative frequency-dependent selection.
What is negative frequency-dependent selection?
Negative frequency-dependent selection occurs when a genotype has increased fitness only when it is rare in the population. As its frequency increases, its fitness decreases, leading to a balancing effect where the rare genotype is favored by selection.
Is negative frequency-dependent selection common?
Yes, negative frequency-dependent selection is actually quite common in nature. It helps maintain genetic diversity by favoring rare genotypes.
What is an example of negative frequency-dependent selection in plants?
An example is the elder flower orchid (Dactylorhiza sambucina) from Europe, which has two color morphs: purple and yellow. The orchid doesn't contain nectar, so pollinators aren't rewarded. However, the rarer color morph has higher reproductive success.
What happens to the frequency of the yellow morph in the elder flower orchid?
As the yellow morph of the elder flower orchid becomes more common, its reproductive success decreases, which is an example of negative frequency-dependent selection. The rare color morph is always favored, and its frequency increases.
What happens over time in the elder flower orchid population?
Over time, the population swings back and forth between the two color morphs, with selection pressure always favoring the rarer color. This results in a balance being maintained between the two color morphs in the population.
What is the outcome of frequency-dependent selection in the elder flower orchid?
The rarer color morph (either purple or yellow) is favored, leading to fluctuating population frequencies of each color. The mean frequency of both morphs is maintained over time due to the selection pressure.
How do you calculate fitness in terms of offspring and survival rate?
Fitness is calculated as absolute fitness, which is the product of the number of offspring and the survival rate of an individual:
Fitness=Offspring×Survival Rate
How do you calculate relative fitness?
Relative fitness compares an individual's fitness to the most fit individual in the population. The most fit individual is assigned a relative fitness of 1. To calculate relative fitness, use the following:
Relative Fitness (w)=
Absolute Fitness of Genotype
/Highest Absolute Fitness
What is mean fitness of a population?
Mean fitness is the average fitness of all individuals in the population. It can be calculated by taking the weighted average of the relative fitness of all genotypes, where the most fit genotype has a relative fitness of 1.
What does delta p represent in modeling selection?
Delta p represents the change in allele frequency between generations. If,
Δp>0, it indicates that the frequency of a particular allele is increasing in the population. postive sslection, genetic drift in small pops, mutations, gene flow, non random mating.
Δp=. 0 allele freq is constant, no evolutionary forces acting upon allele.
Δp<0 allle freq dec, maybe cause of natural selection, genetic drift, or gene flow
What is pleiotropy?
Pleiotropy is when a single gene influences multiple traits or phenotypic characteristics. A mutation in a pleiotropic gene can have wide-ranging effects on an organism.
Why are most traits distributed on a bell curve in quantitative genetics?
Most traits are distributed on a bell curve because they are polygenic (controlled by multiple genes) and influenced by the environment. This results in a normal distribution, with phenotypes clustered around a mean value.
What is the formula for variance in quantitative genetics?
The total variance (Vp) is the sum of environmental variance (Ve) and genetic variance (Vg): Vp=Ve+Vg
Ve is
Variation due to environmental influences
Vg is variation because of genetics, this includes
Vi: Interactive variance (genes interact with each other)
Va: Additive variation (multiple genes contribute additively to the phenotype)
Vd: Dominance variation (due to dominant-recessive allele interactions)
What is the difference between H² (broad sense heritability) and h² (narrow sense heritability)?
H² : Broad sense heritability represents the proportion of the total variance in a trait due to genetic factors (both additive, dominance, and interaction).
h²: Narrow sense heritability measures the proportion of variance in a trait due to additive genetic effects only (i.e., the alleles that contribute to the trait in a straightforward, additive way).
what does a high broad sense heritability indicate (H²)
If H² is high, it indicates the trait is more heritable (closer to 1).
What are the different types of selection in evolutionary biology?
Balancing Selection, Disruptive Selection, Directional Selection, Stabilizing Selection
what is balancing selction
Maintains genetic diversity by favoring the maintenance of multiple alleles.
what is disruptive selection
Selects for extreme phenotypes, causing an increase in variance and potentially leading to a bimodal distribution.
what is directional selection
Favors one extreme phenotype, causing a shift in the mean of the population and possibly reducing variance.
what is stabilizing selection
Selects for average phenotypes, reducing variance but keeping the mean unchanged.
What is the effect of stabilizing selection on the population?
In stabilizing selection, the mean remains the same, but variance decreases as selection favors the average phenotype and eliminates extreme variants.
How does disruptive selection affect variance?
In disruptive selection, the mean remains unchanged, but variance increases as the population is selected against the average phenotype and favors the extremes, leading to a bimodal distribution.
How does directional selection affect the mean and variance?
In directional selection, the mean changes in favor of one extreme, while the variance remains relatively the same. This leads to a shift toward the favored extreme phenotype.
What is the importance of heritability in response to selection?
The response to selection depends on heritability—the higher the heritability ( h²) the faster the response to selection. Traits with high heritability are more likely to show rapid changes in response to selective pressure.
What is Big S in the context of selection?
Big S represents the strength of selection, which is the difference between the mean trait value in the population and the mean trait value in the reproducing individuals. It indicates how strong the selective pressure is on the population.
What is the Breeder's Equation used for?
The Breeder's Equation is used to calculate the response to selection (R) and is given by:
R= H² X big S
Where:
H² = Broad sense heritability
Big S = Strength of selection
This equation helps predict how much a trait will change in the next generation due to selection.
What is the difference between little s and Big S?
Little s: Represents the selection coefficient, which measures the relative fitness of a genotype compared to the most fit genotype.
Big S: Represents the strength of selection, which measures the difference in trait values between the population and the reproducing individuals.
How do you measure variation of quantitative traits in natural populations?
Variation in quantitative traits in natural populations can be measured by comparing the survival of individuals that differ in the trait of interest.
what showed evidence that natural selection can cause measurable changes in traits without human intervention.
Darwin’s finches on the Galapagos Islands showed that natural selection can influence traits like beak size
How do you measure selection through survivorship comparison?
Survivorship comparison involves comparing the survival of individuals with different traits (such as size or beak length). This can be done by measuring the size of a trait (denoted as z) before and after selective pressure. The formula for measuring selection is:
i= [(mean after selection)-(mean before selection)]/ square root(variance in that trait)
mean after selection= Za
mean before selection= Zb
the variance in the phenotype/trait= Vp
What does the measure 𝑖 represent in selection?
The measure 𝑖 represents the intensity of selection, indicating the directional pressure on a population. If 𝑖 is positive, it suggests directional selection is acting on the population, favoring certain phenotypes.
What is the selection gradient?
The selection gradient measures the relationship between the phenotypic value of a trait and the fitness associated with that phenotype. This relationship is estimated by regression analysis and is represented by the slope (beta):
what does a steeper slope mean (beta)
A steeper slope means a stronger relationship between the trait and fitness.
what does the value of beta indicate
If beta is positive, larger phenotypic values are selected for (directional selection).
If beta is negative, the phenotype is disfavored, indicating negative selection (selection against the trait).
What did Peter and Rosemary Grant study on Daphne Major in the Galápagos Islands?
Peter and Rosemary Grant started a research project on the medium ground finch (Geospiza fortis) in 1973. They tracked reproductive success, measured body size, and created genealogies for the finches. The Grants studied heritable variation for traits like beak length and beak depth.
What is the heritability of beak length and beak depth in the medium ground finch?
The heritability (h²) of beak length is 0.65, and the heritability of beak depth is 0.9 in the medium ground finch. Both traits show high heritability, meaning they can be passed down to offspring and are influenced by genetic factors.
How does beak size affect the medium ground finch's diet?
Beak size influences the type of seed the finch can easily handle. Larger beaks are suited for cracking hard seeds from caltrop, while smaller beaks are suited for cracking soft seeds from spurge plants.
What happened on Daphne Major in 1977 during the drought, and how did it affect beak size?
In 1977, a drought on Daphne Major caused most of the spurge seeds (small, soft seeds) to be unavailable. The average beak depth increased from 9.2 mm before the drought to 9.7 mm afterward, as birds with larger beaks were better able to handle the larger, harder caltrop seeds. This is an example of directional selection.
How did beak depth change in the medium ground finch after the 1977 drought?
After the 1977 drought, beak depth in medium ground finches increased, as birds with deeper beaks were more capable of handling the larger, harder seeds that became more abundant during the dry season. Beak depth was found to be heritable in the 1978 offspring.
What happened in 1985 in Daphne Major after heavy rains, and how did it affect beak size?
In 1985, heavy rains caused the spurge plant population to increase. As a result, smaller beaked birds were better suited for eating the small soft seeds from spurge. Beak size in the finch population became more narrow, and having a deep beak was no longer advantageous.
Why did beak length still increase even though it was selected against after the 1977 drought?
Beak length was developmentally correlated with beak depth. Even though beak length was selected against (birds with shorter beaks were favored), beak length still increased because it is developmentally linked to beak depth, which was positively selected for.
What is ecological character displacement, and how did it apply to the medium ground finch?
Ecological character displacement occurs when competition for resources favors traits that reduce overlap between species. In the case of the medium ground finch (G. fortis), the large-beaked finch (G. magnirostris) outcompeted them for large seeds. As a result, the mean beak size in G. fortis decreased over time, and smaller beaked individuals were favored. This is an example of ecological character displacement.
What is the significance of the study on Oldfield mice in the Gulf Coast of the U.S
The study of Oldfield mice in the Gulf Coast supports the theory of evolution by natural selection. The light and dark mice match the backgrounds they inhabit, which suggests that natural selection through visual predation is shaping the color traits of these mice.
How did researchers test whether Oldfield mice color matched their environment due to selective pressure from predators?
Researchers used plasticine models of light and dark Oldfield mice to test the effect of visual predators. They placed the models on soil backgrounds that either matched or didn’t match the color of the model mice. They found that mismatched models were attacked more frequently by predators than the matching models.
What did the researchers find about the proportion of attacks on mismatched versus matching models of Oldfield mice?
Researchers found that mismatched models of Oldfield mice (those not matching the background color) were attacked much more often by predators. The proportion of attacks on mismatched mice was higher compared to the matching mice, indicating that crypsis (color matching with the environment) offers a survival advantage.
How do light and dark Oldfield mice populations vary along the U.S. East Coast and Gulf Coast?
On the Atlantic Coast of Florida and the Gulf Coast, there are populations of light and dark Oldfield mice that match the colors of their respective environments. This indicates directional selection for color matching to avoid predation.
Are the light Oldfield mice in the Gulf Coast and Atlantic Coast more closely related to each other, or are they independently evolved?
Molecular analysis revealed that the light-colored Oldfield mice from the Gulf Coast and Atlantic Coast are more closely related to the dark-colored mice from the same regions, suggesting two independent origins of the light color morph. This supports the idea of independent evolution of the light color due to local predation pressures and crypsis.
What is the significance of directional selection in the case of Oldfield mice and their color morphs?
Directional selection is observed in Oldfield mice because mice with colors matching their backgrounds are less likely to be seen and eaten by predators. Over time, mice with advantageous color traits (light or dark, depending on the environment) are selected for, leading to a change in the population's phenotype toward the more advantageous color variant.
What type of selection is observed in Gall fly populations and why?
Disruptive selection is observed in Gall fly populations because different selective pressures (predators) push the gall size in opposite directions. Large galls are easier for birds to predate, while small galls are more vulnerable to parasitic wasps. As a result, both extremes are favored by selection, leading to two distinct populations.
Q: How do birds and wasps impact gall size in Gall flies?
Birds prefer large galls → easier to access larvae.
Wasps prefer small galls → better for laying eggs.
This results in disruptive selection favoring both extremes.
What happens when both birds and wasps are present in Gall fly environments?
When both are present:
Stabilizing selection occurs (favors intermediate sizes).
If parasitism is stronger: Directional selection favors smaller galls.
What is the Three-spined stickleback fish's armor adaptation related to?
Armor (bony plates/spines) helps protect against large predatory fish.
In freshwater, armor is reduced due to lower predation and nutrient deficiencies.
Why is there a reduction in armor for Three-spined sticklebacks in freshwater?
Lower predation pressure in lakes (fewer large predators).
Nutrient deficiencies in freshwater lakes (low ion concentrations).
What is the genetic cause of reduced armor in Three-spined stickleback populations?
The low-eda allele is responsible.
Recessive allele more common in freshwater.
In marine, the allele is rare.
What happens to Three-spined sticklebacks when they move from marine to freshwater environments?
Armor reduction due to:
Lower predation in freshwater.
Nutrient deficiency (low ions) in freshwater lakes.
Results in evolution of armor reduction.
What is lactase persistence and how is it inherited?
Lactase persistence: Ability to digest milk into adulthood.
Caused by mutations in the LCT gene.
Present in 30% of adults worldwide.
Mutations allow individuals to digest milk sugars (lactose).
Why is lactase persistence advantageous in certain populations?
Domestication of cattle led to milk consumption.
Milk is nutrient-rich → those who could digest it had a survival advantage.
Lactase persistence provides a nutritional advantage in environments with domesticated animals.
What is a selective sweep in relation to lactase persistence?
Selective sweep: Strong selection for a beneficial allele (lactase persistence) causes it to become fixed in a population.
Loci near LCT gene are inherited together in those with lactase persistence.
What is hitchhiking in genetics?
Hitchhiking: The process where nearby alleles increase in frequency due to the selection of a favorable allele (e.g., lactase persistence).
Alleles near the LCT gene are more likely to be inherited together due to their physical proximity on the chromosome.
How do scientists detect evidence of lactase persistence selection in the genome?
Molecular fingerprint left by past selective sweeps can be observed.
How did lactase persistence evolve independently in different populations?
Independent mutations led to lactase persistence in European and African populations.
Genetic evidence supports independent selective sweeps in each population.
How do humans act as selective agents in nature?
Humans influence selection on many species, both prokaryotes and eukaryotes.
Artificial selection: Humans select for traits in plants and animals that are useful or interesting.
Inbreeding in purebred lines can accidentally select for deleterious recessive alleles.
How does artificial selection occur in agriculture?
Cruciferous vegetables (e.g., cabbage, broccoli, cauliflower) are the same species but selected for different traits.
Domesticated crops, like corn (big kernels) and tomatoes (large fruit), have been selected over centuries to be much different from their wild ancestors.
How does human hunting impact selection in wildlife?
Hunting creates selective pressures by favoring traits that allow animals to survive.
Elephants with tusks are targeted by poaching, so tuskless elephants have higher survival and reproductive success.
This has led to mutations causing tuskless elephants to become more common.
How does fishing create selection pressure?
Fishing has caused species like Atlantic cod to undergo directional selection, favoring earlier maturity and smaller body sizes.
Larger fish are often selected against due to fishing practices, leading to declining body size in populations with high fishing pressure.
How does directional selection work in an invasive scenario?
Advantageous allele starts rare.
A new advantageous allele is unlikely to become fixed unless it increases in frequency when rare.
Example: Darwin's finches and beak size.
What is balancing selection?
Keeps genetic diversity at levels higher than expected by chance.
Occurs due to negative frequency-dependent selection or heterozygote advantage.
What is heterozygote advantage?
Heterozygotes have higher fitness than both homozygotes.
Leads to stable polymorphism where both alleles, A1 and A2, are maintained in the population.
What is quantitative genetics?
Study of continuous traits and their evolutionary mechanisms.
How is sample variance calculated?
It measures the difference between individual measurements and the mean.
It assumes population variance, but it's based on sample data since it's not feasible to measure all individuals.
What is ecological character displacement?
Evolution driven by competition for resources.
Traits shared between species evolve to reduce resource overlap (e.g., beak size in birds).
What is crypsis?
Camouflage; animals blend with their background to avoid predators.
What is a homologous sequence?
Sequences derived from a common ancestral gene.
What is hitchhiking in genetics?
Loci on either side of an allele increase in frequency without selection.
What is the difference between orthologs and paralogs?
Orthologs: Homologous sequences in different species, separated by speciation.
Paralogs: Homologous sequences within the same species, separated by gene duplication events.
why do we need to diffrentiate betwen otrhologs and paralogs
the reason for differentiating is that the two copies can have separate evolutionary histories, many not have the same origin.
What is a molecular clock?
Neutral mutations accumulate at a constant rate, correlating to differences between taxa.
Helps in tree reconstruction and calibration of evolutionary timelines.
Caveat: Less accurate for long-diverged taxa.
What is the difference between using molecular and morphological data for reconstructing evolutionary relationships?
Molecular data helps trace back traits, even when morphological data is unavailable.
Morphological data is more informative for identifying speciation events.
What is coalescence in the context of gene sequences?
Coalescence is the merging of homologous gene copies from different individuals to a common ancestor when traced back through generations.
It doesn't imply a single ancestral individual but rather a common ancestor for those alleles.
How does coalescence differ from convergence?
Coalescence refers to the coming together of homologous sequences tracing back in time.
Convergence is the independent evolution of similar traits or sequences in unrelated lineages.
What does it mean for alleles to be homologous?
Homologous alleles are derived from a common ancestral sequence and have descended from the same original genetic source.
How does coalescence work in a population with multiple alleles?
Tracing alleles back in time shows that they may not be passed down directly through generations.
Mutations lead to the emergence of new alleles that eventually coalesce into one of many fixed alleles in the population.
How does coalescence apply to a sequence with a polymorphism (e.g., G → T in BRCA1)?
Polymorphisms like G → T in BRCA1 can be traced back to see when the mutation occurred.
Sequences with ancestral G and derived T are homologous and coalesce at their common ancestral sequence.
What is the process of coalescence when studying multiple sequence copies in a population?
In a population, multiple copies of a sequence can be traced back in time to a common ancestor.
Coalescence occurs when two copies of a sequence eventually trace back to a single common ancestral copy.
Why do gene trees not always equal species trees?
Mutations can occur without speciation.
Genes may not change during speciation, leading to different patterns in gene and species trees.
Example: Human genes have different coalescent times; mitochondrial DNA evolves rapidly, while MX1* evolves slowly.
What does the coalescence time of genes tell us about their evolution?
Mitochondrial DNA has a rapid coalescence time (<0.5 million years), reflecting fast evolution.
MX1 gene* has a slow coalescence time (~8 million years), indicating slow evolution.
What is incomplete lineage sorting?
It occurs when a genetic polymorphism persists through multiple speciation events.
This can cause a different gene tree than the actual species tree, creating confusion in genetic relationships.
How does incomplete lineage sorting affect species relationships?
For example, humans are more closely related to chimps than gorillas.
Incomplete sorting may cause some parts of the human genome to be more closely related to gorillas than chimps, leading to incorrect conclusions about species relationships.
What would happen if there was no incomplete lineage sorting in human genome analysis?
All regions of the human genome would be more similar to chimps than to gorillas or other species.
No incomplete sorting means genetic differences reflect true species relationships.
How can incomplete lineage sorting affect phylogenetic trees?
Incomplete sorting can cause some genomic regions to appear more closely related to the wrong species, which may produce incorrect phylogenetic trees.
Solution: More data is needed to accurately reconstruct the true evolutionary history.
What is the challenge with using a single gene for phylogenetic analysis?
Single gene analysis can produce conflicting results.
Example: 70% of genetic analyses show humans and chimps are more related, but 30% show humans and gorillas are more related, due to using different genes.
What are the pros of molecular phylogenetics compared to morphology-based systematics?
Unambiguous identification of character states (A, T, C, G).
Can use thousands of genetic characters for analysis.
What are the cons of molecular phylogenetics?
Restricted to extant taxa (living species) or recently living.
DNA rarely survives for over 100k years, making ancient DNA analysis difficult.
Harder to distinguish homoplasy (independent mutations) from homology (shared ancestry).
Morphological data is still needed to support molecular data.
What is Maximum Parsimony in molecular phylogenetics?
Max Parsimony minimizes the number of evolutionary changes required to explain the data.
Exons are given more weight than introns because they are less likely to undergo homoplasy.
How does bootstrapping work in Maximum Parsimony?
Bootstrapping involves randomly selecting subsets of characters, redoing the tree with those subsets, and then analyzing the consistency of the results.
If the same relationships appear consistently, the tree has high bootstrap support.
What is the role of morphological data in molecular phylogenetics?
Morphological data is used to support molecular data, especially when distinguishing homoplasy from homology.
Helps ensure the reliability of phylogenetic relationships.
What is Neighbour Joining (NJ) method in phylogenetics?
Neighbour Joining calculates the distance between taxa based on similarities.
Starts with the most closely related taxa.
Quick but less reliable than other methods.
Can use amino acid sequence differences.
What is the advantage and disadvantage of Neighbour Joining (NJ)?
Advantage: Fast, easy for computers to run.
Disadvantage: Less reliable compared to other methods because it doesn't account for ancestral/derived states of characters.
How does the Maximum Likelihood (ML) method work?
ML uses prior knowledge of how mutations occur in DNA.
Model selection is based on known mutation patterns (e.g., mutations at 3rd position of codon are more likely).
For each tree, ML calculates the probability of observing the data given the tree, and assigns a likelihood value to the tree.
Requires significant computing power.
How does the Bayesian method work in phylogenetic reconstruction?
Similar to Maximum Likelihood, but uses inverse probability.
Starts with a tree shape and calculates the probability, then tweaks it to maximize the probability.
Requires significant computing power and time.
What are the key differences between Maximum Likelihood (ML) and Bayesian method?
Both require prior knowledge of mutation models.
ML calculates probability of observing the data given the tree.
Bayesian method starts with a tree and tweaks it to maximize the probability of the tree fitting the data.
Both methods are computationally intensive.
How do researchers decide between phylogenetic methods (NJ, MP, ML, Bayesian)?
ML and Bayesian methods require enormous computational power (days/weeks).
Quick methods like NJ or MP are often run first for initial results.
If multiple methods agree, it gives strong support for a tree.
What is a polymorphism in genetics?
Polymorphism: A common difference in sequence between related species or individuals of the same species.
What is a complication when building molecular phylogenies?
Polymorphisms (genetic differences) are often non-selective, meaning they can arise without natural selection acting on them, complicating tree construction.
What are the pros and cons of using molecular phylogenies?
Pros:
Unambiguous character states (e.g., A, T, C, G)
Can use 100,000s of characters.
Cons:
Restricted to extant taxa (living species)
Need to distinguish between homology and homoplasy (similar traits that are not due to common ancestry).
What does the molecular phylogeny of tetrapods support?
Fossils suggest tetrapods evolved from lobe-finned fish ancestors.
Molecular phylogeny using 251 genes agrees with morphological phylogeny, showing tetrapods' closest living relatives are coelacanths and lungfish.
What does the "Out of Africa" hypothesis propose about human origins?
The "Out of Africa" hypothesis suggests humans originated in Africa.
Molecular phylogenetic analysis shows the greatest genetic variation is found in native African populations, supporting this hypothesis.
What does molecular phylogenetics reveal about the origins of HIV?
HIV is polyphyletic at two levels:
HIV-1 comes from chimpanzee simian immunodeficiency virus (SIV).
HIV-2 comes from sooty mangabey SIV.
HIV-1 jumped into humans twice, once directly from chimpanzees and once from gorillas.
The virus likely entered humans through bushmeat trade, and subtypes can be traced via molecular phylogeny to specific ape/monkey species.
Who proposed the concept of neutral evolution?
Moto Kimura.
What is the core idea of neutral evolution?
Much of the variation in genomes is due to genetic drift rather than natural selection.
What are the two key predictions of neutral evolution?
Mutation accumulation rate is constant and predictable.
Mutations accumulate faster in regions of the genome that don’t affect phenotype.
What type of mutations accumulate faster in neutral evolution?
Synonymous mutations accumulate faster than non-synonymous mutations.
What is the neutral theory in evolutionary biology?
It serves as the null hypothesis for natural selection, proposing that many genetic changes are due to drift.
What is a major prediction from neutral theory?
neutral mutations should accumulate at a roughly constant rate over time.
What was an early piece of evidence supporting neutral theory?
A 1970 study comparing cytochrome c gene differences between pairs of mammalian species
What was the result of the 1970 cytochrome c gene study?
A positive linear relationship was observed between the number of mutations and time since species divergence.
What is the role of calibration in molecular clocks?
Calibration (e.g., via fossils or geographic events) provides a time start point for measuring evolutionary time.
Why do molecular clocks need a calibrated anchor?
Without it, you can measure time passed, but not when an event started
Why can molecular clocks be inaccurate for long-diverged taxa?
Reversals or mutations that revert back to the original base pair can occur.
What happens to sequence differences as species diverge over time?
For closely related species, the slope of differentiation is high, but as divergence time increases, the slope plateaus due to saturation of mutations.
What is the concept of saturation in molecular clocks?
Saturation occurs when new mutations overwrite older ones, causing a plateau in sequence differences after ~10-20 million years.
Is the prediction of a universal molecular clock supported?
No, rates of sequence evolution are not constant across lineages, as factors like generation time and metabolic rate influence divergence rates.
How do body size and metabolic rate affect molecular clock rates?
Sequence divergence rates are negatively correlated with body size (and generation time); endotherms evolve faster than ectotherms.
When are molecular clocks useful in dating events?
When generation times are fast, such as with viruses or bacteria, allowing for recent event dating (e.g., HIV evolution).
How were molecular clocks used to date HIV’s jump from chimpanzees to humans?
By using preserved blood samples and molecular clocks, researchers estimated HIV’s jump to humans occurred between 1883-1925.
How did the European colonization of Africa affect HIV’s jump to humans?
Increased bushmeat trade during colonization likely facilitated the jump of HIV from chimps to humans.
What is neutral theory in molecular evolution?
Neutral theory suggests that most genetic variation in a population is due to genetic drift, not natural selection. It acts as the null hypothesis for detecting natural selection.
How can selective sweeps and hitchhiking sequences provide evidence for natural selection?
Selective sweeps leave molecular evidence of past natural selection through hitchhiking sequences. This evidence typically persists for around 10,000 years
How can researchers detect past natural selection using synonymous and non-synonymous mutations?
Researchers compare synonymous mutations (neutral) and non-synonymous mutations (adaptive). If non-synonymous mutations accumulate faster than synonymous ones, it suggests directional selection.
What does stabilizing selection look like in terms of synonymous and non-synonymous mutations?
In stabilizing selection, there are more synonymous mutations than non-synonymous mutations, as stabilizing selection conserves the gene's function.
Why do footprints of selection require strong selection pressures to be visible?
Weak selection pressures may not leave a noticeable trace, so strong selection is necessary to detect footprints of selection in genetic data.
How is genome size related to prokaryotes and eukaryotes?
Prokaryotes (bacteria) have streamlined genomes with most of the DNA coding for proteins, while eukaryotes often have larger, more complex genomes, including non-coding regions like pseudogenes.
Why do some prokaryotes have very small genomes?
Some prokaryotes, especially intracellular endosymbionts, have small genomes because they rely on their host for many functions and have abandoned many genes.
What contributes to the "bloated" genomes of eukaryotes?
Eukaryotes often have pseudogenes, parasitic DNA (e.g., viral remnants), and other non-coding regions, which contribute to the larger, more complex genome
How does the size of an organism's genome relate to its cell division time?
The time it takes for a cell to divide is positively related to genome size, as more DNA requires more time to replicate during cell division.
Why do some organisms have smaller genomes?
Organisms with smaller genomes may have reduced DNA because they rely on a host organism for some biological functions, often seen in endosymbionts.